Microbiologist Professor Hugh Pennington said tens of millions of pounds from UK research councils helped sustain cutting-edge science north of the Border, money which could dry up if Scotland voted Yes in the 2014 referendum.
He told the Sunday Herald: "Key to the success of British science has been the unimpeded two-way traffic of ideas, money and people across the Border. So, I believe that if Scotland leaves the UK, its science will take a knock."
His comments echo those of Labour peer Lord Winston, a scientific adviser to the Scottish Government, and Tory Science Minister David Willetts, who warned of a "brain drain" if lower research funding made Scottish institutions less attractive after independence.
Pennington, 74, emeritus professor of bacteriology at Aberdeen, having retired in 2003 has also helped advise the Scottish Labour Party on health policy. He said the Medical Research Council (MRC), which last year spent £760 million on research in the UK, was "crucial to the success of Scottish universities". Four of its 25 specialised research units are in Scotland, as are four of 27 larger research centres.
Pennington said: "The MRC exemplifies why British research is so successful. It claims 29 Nobel Prizes. Its practical achievements have been outstanding, including the discovery of the influenza virus, penicillin, the structure of DNA, monoclonal antibodies, and MRI [scans].
"It spends big in Scotland. There are currently 43 grants from the body to the likes of Aberdeen, Dundee, Edinburgh and Glasgow Universities worth £31,418,000.
"Four million pounds has been committed to the University of Glasgow Centre for Virus Research and a £36m investment to March 2015 has been made at the University of Edinburgh Institute of Genetics and Molecular Medicine, which has more than 200 MRC staff and students."
Pennington said the MRC was not the sole research council funding Scottish science, and that in 2010-11 the £67m received by Edinburgh from various research councils accounted for nearly half of all its external research grants.
"It is clear that Scotland does extremely well in research councils funding," he said. "The current budget for this UK money is more than £3 billion. It covers the full spectrum of academic disciplines:the medical and biological sciences; astronomy; physics; chemistry and engineering; social sciences; economics; environmental sciences; and the arts and humanities. I await with interest how the 'Yes' proponents propose to continue not only the continued access to UK research councils funding, but the competitive drive brought by bidding for it. Better together for science, surely."
A spokesman for the University and College Union (UCU) Scotland said: "We have concerns that with independence we might see a decrease in research funding, but we are very unclear about what is going to happen at the moment."
A Scottish Government spokeswoman said: "Scotland has an unrivalled record of success in attracting funding, reflecting the excellence and global reputation of our universities, and that will continue with independence.
"We fully understand the importance of stability in long-term funding for world-class researchers."